Jonathan, in an official statement released by his office, sacked the chiefs of the country's army, navy and air force, who have been waging the battle against the Boko Haram Islamists' insurgency in the north of the country.
New officers have been nominated in their place, he added.
Human rights lawyer Festus Keyamo last year mounted a legal challenge to the appointments, arguing they were done without the approval of the national assembly, as demanded by the constitution.
The law intends "to subject the armed forces to civil authority", Keyamo said, adding that neither the president nor the service chiefs were constitutionally superior to the national assembly.
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In a January 7 letter to Jonathan and national assembly leaders, Keyamo gave a 14-day ultimatum to the government to comply with the court ruling.
Failure to do so would see him move the courts "to compel compliance", he added.
The service chiefs "were all appointed without the confirmation of the national assembly. Their appointments are therefore null and void ab initio (from the start)", he stated.
"My appeal to all Nigerians is not to be afraid to approach the courts to ventilate your grievance if government has committed any illegality," he told AFP.